pharmaverse / pharmaverse/logrx
Bug: functions passed to `rlang::exprs` in an R script are not found
@bms63 is already working on this.
Since Jan 16, 2025.
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Description
What happened?
Hi, and thanks for a great package.
Running logrx::axecute from a clean session on the admiral adsl script (https://pharmaverse.github.io/admiral/articles/adsl.html) results in an Error:
Caused by error in `format_eosstt()`:
! could not find function "format_eosstt"
A reproducible example with a smaller script is provided bellow.
Thank you
Session Information
R version 4.4.1 (2024-06-14 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 10 x64 (build 19045)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 LC_MONETARY=English_United States.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8
time zone: Europe/Budapest
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] pharmaversesdtm_1.0.0 dplyr_1.1.4 admiral_1.1.1
loaded via a namespace (and not attached):
[1] utf8_1.2.4 generics_0.1.3 tidyr_1.3.1 renv_1.0.9 tcltk_4.4.1 xml2_1.3.6 stringi_1.8.4 hms_1.1.3 digest_0.6.35 magrittr_2.0.3
[11] timechange_0.3.0 fastmap_1.2.0 processx_3.8.4 sessioninfo_1.2.2 backports_1.5.0 ps_1.7.6 promises_1.3.0 admiraldev_1.1.0 purrr_1.0.2 fansi_1.0.6
[21] lintr_3.1.2 lazyeval_0.2.2 cli_3.6.2 shiny_1.8.1.1 rlang_1.1.3 crayon_1.5.2 remotes_2.5.0 withr_3.0.0 tools_4.4.1 logrx_0.3.1
[31] httpuv_1.6.15 vctrs_0.6.5 waiter_0.2.5 cyclocomp_1.1.1 R6_2.5.1 mime_0.12 lifecycle_1.0.4 lubridate_1.9.3 stringr_1.5.1 miniUI_0.1.1.1
[41] pkgconfig_2.0.3 desc_1.4.3 callr_3.7.6 rex_1.2.1 pillar_1.9.0 later_1.3.2 data.table_1.15.4 glue_1.7.0 Rcpp_1.0.12 tibble_3.2.1
[51] tidyselect_1.2.1 rstudioapi_0.16.0 xtable_1.8-4 htmltools_0.5.8.1 compiler_4.4.1
Reproducible Example
Create an adsl_script.R with following contents:
library(admiral)
library(dplyr, warn.conflicts = FALSE)
library(pharmaversesdtm)
data("dm")
data("ds")
dm <- convert_blanks_to_na(dm)
ds <- convert_blanks_to_na(ds)
adsl <- dm %>%
select(-DOMAIN)
format_eosstt <- function(x) {
case_when(
x %in% c("COMPLETED") ~ "COMPLETED",
x %in% c("SCREEN FAILURE") ~ NA_character_,
TRUE ~ "DISCONTINUED"
)
}
adsl <- adsl %>%
derive_vars_merged(
dataset_add = ds,
by_vars = exprs(STUDYID, USUBJID),
filter_add = DSCAT == "DISPOSITION EVENT",
new_vars = exprs(EOSSTT = format_eosstt(DSDECOD)),
missing_values = exprs(EOSSTT = "ONGOING")
)
from a clean R session create the log for the script:
rm(list = ls())
logrx::axecute(file = "adsl_script.R",
log_name = "adsl_script.log")
the log will contain:
--------------------------------------------------------------------------------
- Errors and Warnings -
--------------------------------------------------------------------------------
Errors:
In argument: `EOSSTT = format_eosstt(DSDECOD)`.
Warnings:
Full log contents:
--------------------------------------------------------------------------------
- logrx Metadata -
--------------------------------------------------------------------------------
This log was generated using logrx 0.3.1
logrx package version: 0.3.1
logrx build: CRAN (R 4.4.1)
logrx link to repository: https://github.com/pharmaverse/logrx
--------------------------------------------------------------------------------
- User and File Information -
--------------------------------------------------------------------------------
User: missu
File Name: adsl_script.R
File Path: D:/R/risk
File HashSum: 570a9f5e01c1f82d55098eacbea5c7b576540d74
--------------------------------------------------------------------------------
- Session Information -
--------------------------------------------------------------------------------
─ Session info ─────────────────────────────────────────────────────────────────
setting value
version R version 4.4.1 (2024-06-14 ucrt)
os Windows 10 x64 (build 19045)
system x86_64, mingw32
ui RStudio
language (EN)
collate English_United States.utf8
ctype English_United States.utf8
tz Europe/Budapest
date 2024-10-03
rstudio 2024.09.0+375 Cranberry Hibiscus (desktop)
pandoc 3.2 @
C:\\PROGRA~1\\RStudio\\RESOUR~1\\app\\bin\\quarto\\bin\\tools\\pandoc.exe
─ Packages ─────────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
admiral * 1.1.1 2024-06-17 [1] CRAN (R 4.4.1)
admiraldev 1.1.0 2024-06-06 [1] CRAN (R 4.4.1)
backports 1.5.0 2024-05-23 [1] CRAN (R 4.4.0)
callr 3.7.6 2024-03-25 [1] CRAN (R 4.4.0)
cli 3.6.2 2023-12-11 [1] CRAN (R 4.4.0)
crayon 1.5.2 2022-09-29 [1] CRAN (R 4.4.0)
cyclocomp 1.1.1 2023-08-30 [1] CRAN (R 4.4.1)
data.table 1.15.4 2024-03-30 [1] CRAN (R 4.4.0)
desc 1.4.3 2023-12-10 [1] CRAN (R 4.4.0)
digest 0.6.35 2024-03-11 [1] CRAN (R 4.4.0)
dplyr * 1.1.4 2023-11-17 [1] CRAN (R 4.4.1)
fansi 1.0.6 2023-12-08 [1] CRAN (R 4.4.0)
fastmap 1.2.0 2024-05-15 [1] CRAN (R 4.4.0)
generics 0.1.3 2022-07-05 [1] CRAN (R 4.4.0)
glue 1.7.0 2024-01-09 [1] CRAN (R 4.4.0)
hms 1.1.3 2023-03-21 [1] CRAN (R 4.4.0)
htmltools 0.5.8.1 2024-04-04 [1] CRAN (R 4.4.0)
httpuv 1.6.15 2024-03-26 [1] CRAN (R 4.4.0)
later 1.3.2 2023-12-06 [1] CRAN (R 4.4.0)
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.4.1)
lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.4.0)
lintr 3.1.2 2024-03-25 [1] CRAN (R 4.4.1)
logrx 0.3.1 2024-04-12 [1] CRAN (R 4.4.1)
lubridate 1.9.3 2023-09-27 [1] CRAN (R 4.4.0)
magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.4.0)
mime 0.12 2021-09-28 [1] CRAN (R 4.4.0)
miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.4.0)
pharmaversesdtm * 1.0.0 2024-06-06 [1] CRAN (R 4.4.1)
pillar 1.9.0 2023-03-22 [1] CRAN (R 4.4.0)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.4.0)
processx 3.8.4 2024-03-16 [1] CRAN (R 4.4.0)
promises 1.3.0 2024-04-05 [1] CRAN (R 4.4.0)
ps 1.7.6 2024-01-18 [1] CRAN (R 4.4.0)
purrr 1.0.2 2023-08-10 [1] CRAN (R 4.4.0)
R6 2.5.1 2021-08-19 [1] CRAN (R 4.4.0)
Rcpp 1.0.12 2024-01-09 [1] CRAN (R 4.4.0)
remotes 2.5.0 2024-03-17 [1] CRAN (R 4.4.0)
renv 1.0.9 2024-09-23 [1] CRAN (R 4.4.1)
rex 1.2.1 2021-11-26 [1] CRAN (R 4.4.1)
rlang 1.1.3 2024-01-10 [1] CRAN (R 4.4.0)
rstudioapi 0.16.0 2024-03-24 [1] CRAN (R 4.4.0)
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.4.0)
shiny 1.8.1.1 2024-04-02 [1] CRAN (R 4.4.0)
stringi 1.8.4 2024-05-06 [1] CRAN (R 4.4.0)
stringr 1.5.1 2023-11-14 [1] CRAN (R 4.4.0)
tibble 3.2.1 2023-03-20 [1] CRAN (R 4.4.0)
tidyr 1.3.1 2024-01-24 [1] CRAN (R 4.4.0)
tidyselect 1.2.1 2024-03-11 [1] CRAN (R 4.4.0)
timechange 0.3.0 2024-01-18 [1] CRAN (R 4.4.0)
utf8 1.2.4 2023-10-22 [1] CRAN (R 4.4.0)
vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.4.0)
waiter 0.2.5 2022-01-03 [1] CRAN (R 4.4.1)
withr 3.0.0 2024-01-16 [1] CRAN (R 4.4.0)
xml2 1.3.6 2023-12-04 [1] CRAN (R 4.4.0)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.4.0)
[1] C:/Users/missu/AppData/Local/R/win-library/4.4
[2] C:/Program Files/R/R-4.4.1/library
─ External software ────────────────────────────────────────────────────────────
setting value
cairo 1.18.0
cairoFT
pango
png 1.6.42
jpeg 9.6
tiff LIBTIFF, Version 4.6.0
tcl 8.6.13
curl 8.6.0
zlib 1.3.1
bzlib 1.0.8, 13-Jul-2019
xz 5.4.6
deflate 1.19
PCRE 10.43 2024-02-16
ICU 74.2
TRE TRE 0.8.0 R_fixes (BSD)
iconv win_iconv
readline
BLAS
lapack
lapack_version 3.12.0
─ Python configuration ─────────────────────────────────────────────────────────
Python is not available
────────────────────────────────────────────────────────────────────────────────
--------------------------------------------------------------------------------
- Masked Functions -
--------------------------------------------------------------------------------
function `ts` from {package:stats} by package:pharmaversesdtm
function `cm` from {package:grDevices} by package:pharmaversesdtm
function `%>%` from {package:admiral} by package:dplyr
function `desc` from {package:admiral} by package:dplyr
function `filter` from {package:stats} by package:dplyr
function `lag` from {package:stats} by package:dplyr
function `intersect` from {package:base} by package:dplyr
function `setdiff` from {package:base} by package:dplyr
function `setequal` from {package:base} by package:dplyr
function `union` from {package:base} by package:dplyr
function `plot` from {package:base} by package:graphics
function `body<-` from {package:base} by package:methods
function `kronecker` from {package:base} by package:methods
--------------------------------------------------------------------------------
- Used Package and Functions -
--------------------------------------------------------------------------------
{!!! NOT FOUND !!!} format_eosstt
{package:admiral} convert_blanks_to_na, derive_vars_merged, exprs
{package:base} library, c, %in%
{package:dplyr} %>%, select, case_when
{package:utils} data
--------------------------------------------------------------------------------
- Program Run Time Information -
--------------------------------------------------------------------------------
Start time: 2024-10-03 07:16:26 CEST
End time: 2024-10-03 07:16:27 CEST
Run time: 1 seconds
--------------------------------------------------------------------------------
- Errors and Warnings -
--------------------------------------------------------------------------------
Errors:
In argument: `EOSSTT = format_eosstt(DSDECOD)`.
Warnings:
--------------------------------------------------------------------------------
- Messages, Output, and Result -
--------------------------------------------------------------------------------
Messages:
Output:
Result:
NULL
--------------------------------------------------------------------------------
- Log Output File -
--------------------------------------------------------------------------------
Log name: adsl_script.log
Log path: D:/R/risk
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